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Structure of HPK1 with C5 bound at its active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other internal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 not provided by author
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.12 α = 90 b = 75.87 β = 99.48 c = 86.06 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 91 PIXEL DECTRIS PILATUS3 S 6M 2019-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 44.5 99.6 0.131 0.158 0.087 0.973 8.9 3.3 25468
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.3 0.639 0.758 0.405 0.791 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 35 24210 1234 99.43 0.22727 0.22477 0.2291 0.27615 0.2742 RANDOM 49.053
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.92 3.18 -2.72 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.058 r_dihedral_angle_1_deg 6.139 r_dihedral_angle_2_deg 5.152 r_long_range_B_refined 4.021 r_long_range_B_other 4.02 r_scangle_other 1.66 r_mcangle_it 1.488 r_mcangle_other 1.487 r_scbond_it 0.967 r_scbond_other 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.058 r_dihedral_angle_1_deg 6.139 r_dihedral_angle_2_deg 5.152 r_long_range_B_refined 4.021 r_long_range_B_other 4.02 r_scangle_other 1.66 r_mcangle_it 1.488 r_mcangle_other 1.487 r_scbond_it 0.967 r_scbond_other 0.958 r_angle_refined_deg 0.925 r_mcbond_it 0.893 r_mcbond_other 0.893 r_angle_other_deg 0.327 r_chiral_restr 0.045 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4514 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing